PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies

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PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies is …
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scholarly articleQ13442814

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P356DOI10.1093/NAR/GKS406
P932PMC publication ID3439882
P698PubMed publication ID22584627
P5875ResearchGate publication ID224957446

P50authorRobert A EdwardsQ56810780
Ramy K. AzizQ30505462
P2093author name stringSajia Akhter
P2860cites workA Mathematical Theory of CommunicationQ724029
Prophinder: a computational tool for prophage prediction in prokaryotic genomes.Q51895172
Intrastrand parity rules of DNA base composition and usage biases of synonymous codons.Q52209838
Skewed oligomers and origins of replication.Q52232869
Properties of a general model of DNA evolution under no-strand-bias conditions.Q52878851
Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus.Q54548221
Prophage lambda at unusual chromosomal locations. I. Location of the secondary attachment sites and the properties of the lysogensQ69164900
Use of an ordered cosmid library to deduce the genomic organization of Mycobacterium lepraeQ70592227
Insights on Evolution of Virulence and Resistance from the Complete Genome Analysis of an Early Methicillin-Resistant Staphylococcus aureus Strain and a Biofilm-Producing Methicillin-Resistant Staphylococcus epidermidis StrainQ22065445
The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of riceQ22065983
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this speciesQ22065989
The complete genome sequence of Mycobacterium bovisQ22066275
Complete genome sequence of an M1 strain of Streptococcus pyogenesQ22066334
Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistanceQ22066348
The complete genome sequence of Mycobacterium avium subspecies paratuberculosisQ22066352
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7Q22122385
Identifying Important Risk Factors for Survival in Kidney Graft Failure Patients Using Random Survival ForestsQ22673963
Analyzing genomes with cumulative skew diagramsQ24498116
Comparative genomics of Salmonella enterica serovar Typhi strains Ty2 and CT18Q24554266
Comparative genomic analysis of 60 Mycobacteriophage genomes: genome clustering, gene acquisition, and gene sizeQ24634617
Prophage genomicsQ24673108
Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequencesQ24674211
Genome plasticity of BCG and impact on vaccine efficacyQ24674276
Basic local alignment search toolQ25938991
The complete genome sequence of Escherichia coli K-12Q27860542
A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferiQ28144621
Genome sequence of Staphylococcus aureus strain Newman and comparative analysis of staphylococcal genomes: polymorphism and evolution of two major pathogenicity islandsQ28493270
Asymmetric substitution patterns in the two DNA strands of bacteriaQ29618276
Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes.Q33214624
Contribution of exogenous genetic elements to the group A Streptococcus metagenomeQ33295386
Identification of prophages in bacterial genomes by dinucleotide relative abundance differenceQ33306681
Genome landscapes and bacteriophage codon usageQ33332469
Mobile genetic elements in the genome of the beneficial rhizobacterium Pseudomonas fluorescens Pf-5.Q33399917
Accessing the SEED genome databases via Web services API: tools for programmersQ33603751
Preferential orientation of natural lambdoid prophages and bacterial chromosome organizationQ34776786
The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolatesQ34803749
ACLAME: a CLAssification of Mobile genetic ElementsQ34932251
Prophages and bacterial genomics: what have we learned so far?Q35187156
Lambdoid phages as elements of bacterial genomes (integrase/phage21/Escherichia coli K-12/icd gene)Q35611758
Characterization of the ELPhiS prophage from Salmonella enterica serovar Enteritidis strain LK5.Q35817097
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescensQ37282936
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferencesQ37425283
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenesQ39111241
Computational identification of operons in microbial genomesQ39860961
The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomesQ40243266
Structural analysis of the actinophae ФC31 attachment siteQ40507422
Viral integration and excision: structure of the lambda att sitesQ40804250
Comparative DNA analysis across diverse genomes.Q45934068
Post-proteomic identification of a novel phage-encoded streptodornase, Sda1, in invasive M1T1 Streptococcus pyogenesQ48170337
P275copyright licenseCreative Commons Attribution-NonCommercial 3.0 UnportedQ18810331
P6216copyright statuscopyrightedQ50423863
P433issue16
P407language of work or nameEnglishQ1860
P304page(s)e126
P577publication date2012-05-14
P1433published inNucleic Acids ResearchQ135122
P1476titlePhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies
P478volume40

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cites work (P2860)
Q39382890A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements
Q49577359A Practical Guide for Comparative Genomics of Mobile Genetic Elements in Prokaryotic Genomes
Q57798627A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage
Q33950908A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
Q35910566A novel chimeric prophage vB_LdeS-phiJB from commercial Lactobacillus delbrueckii subsp. bulgaricus
Q41490282A novel inducible prophage from the mycosphere inhabitant Paraburkholderia terrae BS437.
Q42275615AnCo3, a New Member of the Emerging Family of Phage-Like Plasmids
Q34542652Applying Shannon's information theory to bacterial and phage genomes and metagenomes
Q37589201Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences.
Q41845229Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences.
Q38211018Bacteriophages of leuconostoc, oenococcus, and weissella
Q57292667Bacteriophages: A Therapy Concept against Multi-Drug-Resistant Bacteria
Q89620887CRISPR-Cas Systems and the Paradox of Self-Targeting Spacers
Q40582033Characterization of Functional Prophages in Clostridium difficile.
Q40136737Characterization of Sinorhizobium sp. LM21 Prophages and Virus-Encoded DNA Methyltransferases in the Light of Comparative Genomic Analyses of the Sinorhizobial Virome
Q64019871Characterization of the transcriptome of Haloferax volcanii, grown under four different conditions, with mixed RNA-Seq
Q67311490Characterization of the virome of Paracoccus spp. (Alphaproteobacteria) by combined in silico and in vivo approaches.
Q40936712CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Q37539160Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates.
Q97521171Comparative Genomics of Acinetobacter baumannii Clinical Strains From Brazil Reveals Polyclonal Dissemination and Selective Exchange of Mobile Genetic Elements Associated With Resistance Genes
Q43121056Comparative Genomics of Pathogenic and Nonpathogenic Strains of Xanthomonas arboricola Unveil Molecular and Evolutionary Events Linked to Pathoadaptation.
Q45253895Comparative analysis of prophages in Streptococcus mutans genomes
Q89830782Comparative genomic analysis of Proteus spp. isolated from tree shrews indicated unexpectedly high genetic diversity
Q34079190Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions
Q28681771Comparison of 26 sphingomonad genomes reveals diverse environmental adaptations and biodegradative capabilities
Q90155465Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis
Q90469005Complete Genome Sequence of Pediococcus pentosaceus Strain GDIAS 001
Q64108085Complete Genome Sequence of sp. Strain TH2012, Isolated from Shrimp in a Cultivation Pond Exhibiting Early Mortality Syndrome
Q42205421Complete Genome Sequences of Two Phage-Like Plasmids Carrying the CTX-M-15 Extended-Spectrum β-Lactamase Gene
Q92833589Complete genome sequence of a marine-sediment-derived bacterial strain Bacillus velezensis SH-B74, a cyclic lipopeptides producer and a biopesticide
Q97521132Computational approaches in viral ecology
Q38666460Computational approaches to predict bacteriophage-host relationships.
Q40734728Computational prospecting the great viral unknown.
Q42243153Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera.
Q34433589Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens
Q90027369Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes
Q92432604Defining the human gut host-phage network through single-cell viral tagging
Q61796379Draft Genome Sequence of Chromatium okenii Isolated from the Stratified Alpine Lake Cadagno
Q93012460EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing
Q42196057Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics
Q28087251Emerging methods to study bacteriophage infection at the single-cell level
Q99591420Evolutionary Study of the Crassphage Virus at Gene Level
Q52604672Expert Opinion on Three Phage Therapy Related Topics: Bacterial Phage Resistance, Phage Training and Prophages in Bacterial Production Strains.
Q38102667Explaining microbial phenotypes on a genomic scale: GWAS for microbes
Q37508193Factors behind junk DNA in bacteria
Q35070691Functional environmental screening of a metagenomic library identifies stlA; a unique salt tolerance locus from the human gut microbiome.
Q98771854Gene Duplications in the Genomes of Staphylococci and Enterococci
Q93115342Generation of a Prophage-Free Variant of the Fast-Growing Bacterium Vibrio natriegens
Q58556368Genome Structure of the Opportunistic Pathogen () and Identification of Putative Virulence Factors
Q40238989Genome and epigenome of a novel marine Thaumarchaeota strain suggest viral infection, phosphorothioation DNA modification and multiple restriction systems.
Q40178164Genome dynamics and evolution of Salmonella Typhi strains from the typhoid-endemic zones
Q42372731Genome of Ca. Pandoraea novymonadis, an Endosymbiotic Bacterium of the Trypanosomatid Novymonas esmeraldas
Q40264697Genome sequencing and analysis of Salmonella enterica serovar Typhi strain CR0063 representing a carrier individual during an outbreak of typhoid fever in Kelantan, Malaysia
Q40176044Genome-wide-analyses of Listeria monocytogenes from food-processing plants reveal clonal diversity and date the emergence of persisting sequence types
Q35650961Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum
Q36341282Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil
Q57252321Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14
Q30376979Genomic and Functional Portrait of a Highly Virulent, CTX-M-15-Producing H30-Rx Subclone of Escherichia coli Sequence Type 131.
Q64065478Host Taxon Predictor - A Tool for Predicting Taxon of the Host of a Newly Discovered Virus
Q39788901HostPhinder: A Phage Host Prediction Tool
Q90524318Identification and Characterization of the First Virulent Phages, Including a Novel Jumbo Virus, Infecting Ochrobactrum spp
Q46843568Insights into organohalide respiration and the versatile catabolism of Sulfurospirillum multivorans gained from comparative genomics and physiological studies
Q47163488Insights into origin and evolution of α-proteobacterial gene transfer agents
Q97530593Insights into the dynamics between viruses and their hosts in a hot spring microbial mat
Q38821898Intriguing Interaction of Bacteriophage-Host Association: An Understanding in the Era of Omics
Q118110726Isolation and Genomic Characteristics of Cat-Borne Campylobacter felis sp. nov. and Sheep-Borne Campylobacter ovis sp. nov
Q42066107Isolation and Genomic Characterization of 'Desulfuromonas soudanensis WTL', a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine
Q46621519Kullback Leibler divergence in complete bacterial and phage genomes.
Q92795353Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains
Q34569191Leptospiral pathogenomics
Q35829441Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34melT.
Q39177652Lysogeny in nature: mechanisms, impact and ecology of temperate phages
Q64271021May the Phage be With You? Prophage-Like Elements in the Genomes of Soft Rot : spp. and spp
Q30641042Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data
Q31133755MetaPhinder-Identifying Bacteriophage Sequences in Metagenomic Data Sets
Q64076925Mining, analyzing, and integrating viral signals from metagenomic data
Q38657588Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
Q64120783Nucleotide Second Messenger-Based Signaling in Extreme Acidophiles of the Species Complex: Partition Between the Core and Variable Gene Complements
Q34504150Orthologous gene clusters and taxon signature genes for viruses of prokaryotes
Q92074567PHANOTATE: a novel approach to gene identification in phage genomes
Q47898909PHAST, PHASTER and PHASTEST: Tools for finding prophage in bacterial genomes
Q37182130PHASTER: a better, faster version of the PHAST phage search tool
Q64913131PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning.
Q50036533Phage Genome Annotation Using the RAST Pipeline.
Q59360291Phage Therapy: What Have We Learned?
Q47382973Phage hunters: Computational strategies for finding phages in large-scale 'omics datasets.
Q57191844Phage puppet masters of the marine microbial realm
Q37658065PhagePhisher: a pipeline for the discovery of covert viral sequences in complex genomic datasets
Q60949673PhageWeb - Web Interface for Rapid Identification and Characterization of Prophages in Bacterial Genomes
Q93109078Phages and Human Health: More Than Idle Hitchhikers
Q64109044Phages for Phage Therapy: Isolation, Characterization, and Host Range Breadth
Q101469937Phenotypic and genomic analysis of isopropanol and 1,3-propanediol producer Clostridium diolis DSM 15410
Q59547518Phenotypic and genomic comparison of Photorhabdus luminescens subsp. laumondii TT01 and a widely used rifampicin-resistant Photorhabdus luminescens laboratory strain
Q61443179Phylogenetic relationship of prophages is affected by CRISPR selection in Group A Streptococcus
Q39824116Phylogenomic networks reveal limited phylogenetic range of lateral gene transfer by transduction
Q91578164Predicting virus-host association by Kernelized logistic matrix factorization and similarity network fusion
Q90437976ProphET, prophage estimation tool: A stand-alone prophage sequence prediction tool with self-updating reference database
Q92203003Prophage Hunter: an integrative hunting tool for active prophages
Q35132855Prophage-like elements present in Mycobacterium genomes
Q58610618Quantifying the changes in genetic diversity within sequence-discrete bacterial populations across a spatial and temporal riverine gradient
Q35065741RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
Q59274011Relating Phage Genomes to Population Structure: General Steps Using Whole-Genome Sequencing Data
Q58758056Role of plasmid plasticity and mobile genetic elements in the entomopathogen Bacillus thuringiensis serovar israelensis
Q30485765SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
Q35275357Salmonella phages and prophages: genomics, taxonomy, and applied aspects
Q37650275Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay
Q34090764Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition
Q30830810Silencing of cryptic prophages in Corynebacterium glutamicum
Q36178838Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton
Q116816762Species classification and novel plasmid identifications in Arcobacter cryaerophilus and Arcobacter cryaerophilus-like organisms
Q40463266Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium.
Q96609251The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics
Q41676275The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes
Q60947174The Human Gut Virome in Hypertension
Q54393165The purity measure for genomic regions leads to horizontally transferred genes.
Q64133058The use of next generation sequencing for improving food safety: Translation into practice
Q55363696Transcription profiling of butanol producer Clostridium beijerinckii NRRL B-598 using RNA-Seq.
Q58559766Transcriptome and comparative genomics analyses reveal new functional insights on key determinants of pathogenesis and interbacterial competition in and spp
Q38690628VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
Q35650782VirSorter: mining viral signal from microbial genomic data
Q40709040Viral dark matter and virus-host interactions resolved from publicly available microbial genomes
Q35209768Viral tagging reveals discrete populations in Synechococcus viral genome sequence space.
Q90083434Whole-Genome Sequence of Corynebacterium xerosis Strain GS1, Isolated from Yak in Gansu Province, China
Q36000537Whole-Genome Sequencing Allows for Improved Identification of Persistent Listeria monocytogenes in Food-Associated Environments

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